The present invention relates to the use of species-specific primers in polymerase chain reaction assays for the detection of Rhizoctonia cerealis, a fungal pathogen of wheat. The use of these primers enables the monitoring of disease development in plant populations.
Diseases in plants cause considerable crop loss from year to year resulting both in economic deprivation to farmers and, in many parts of the world, to shortfalls in the nutritional provision for local populations. The widespread use of fungicides has provided considerable security against plant pathogen attack. However, despite 1 billion worth of expenditure on fungicides, worldwide crop losses amounted to approximately 10% of crop value in 1981 (James, 1981; Seed Sci. and Technol. 9: 679-685).
The severity of the destructive process of disease depends on the aggressiveness of the pathogen and the response of the host. One aim of most plant breeding programs is to increase the resistance of host plants to disease. Typically, different races of pathogens interact with different varieties of the same crop species differentially, and many sources of host resistance only protect against specific pathogen races. Furthermore, some pathogen races show early signs of disease symptoms, but cause little damage to the crop. Jones and Clifford (1983; Cereal Diseases, John Wiley) report that virulent forms of the pathogen are expected to emerge in the pathogen population in response to the introduction of resistance into host cultivars and that it is therefore necessary to monitor pathogen populations. In addition, there are several documented cases of the evolution of fungal strains that are resistant to particular fungicides. As early as 1981, Fletcher and Wolfe (1981; Proc. 1981 Brit. Crop Prot. Conf.) contended that 24% of the powdery mildew populations from spring barley and 53% from winter barley showed considerable variation in response to the fungicide triadimenol and that the distribution of these populations varied between varieties, with the most susceptible variety also giving the highest incidence of less susceptible types. Similar variation in the sensitivity of fungi to fungicides has been documented for wheat mildew (also to triadimenol), Botrytis (to benomyl), Pyrenophora (to organomercury), Pseudocercosporella (to MBC-type fungicides) and Mycosphaerella fijiensis to triazoles to mention just a few (Jones and Clifford; Cereal Diseases, John Wiley, 1983).
Wheat is currently the most important agricultural commodity in international markets and occupies about 20% of the world""s farmed land (1977; Compendium of Wheat Diseases, Amer. Phytopath. Soc. page 1). Eightly percent of the world""s supply of wheat is grown in North America, Europe, China, and the Soviet Union. Approximately 20% of the worldwide production of wheat is lost to disease annually.
Sharp eyespot is caused by Rhizoctonia cerealis van der Hoeven (teleomorph Ceratobasidium cereale Murray and Burpee) and occurs on wheat, barley, oat and rye (1977; Compendium of Wheat Diseases, Amer. Phytopath. Soc. Page 50). Some isolates of the pathogen are also capable of infecting turfgrass causing yellow patch. Severe wheat infections cause premature ripening and lodging, thereby effecting yield. There are presently no known sharp eyespot-resistant cultivars.
In view of the above, there is a real need for the development of technology that will allow the identification of specific fungal pathogens early in the infection process. By identifying the specific pathogen before disease symptoms become evident in the crop stand, the agriculturist can assess the likely effects of further development of the pathogen in the crop variety in which it has been identified and can choose an appropriate fungicide if such application is deemed necessary.
The present invention is drawn to methods of identification of different pathotypes of plant pathogenic fungi. The invention provides Internal Transcribed Spacer (ITS) DNA sequences that show variability between different fungal pathotypes. Such DNA sequences are useful in the method of the invention as they can be used to derive primers for use in polymerase chain reaction (PCR)-based diagnostic assays. These primers generate unique fragments in PCR reactions in which the DNA template is provided by specific fungal pathotypes and can thus be used to identify the presence or absence of specific pathotypes in host plant material before the onset of disease symptoms.
In a preferred embodiment, the invention provides ITS1 and ITS2 DNA sequences (e.g., SEQ ID NO:17-26) for the pathogen Rhizoctonia cerealis. In another preferred embodiment, the invention provides ITS-derived diagnostic primers (e.g., SEQ ID NO:7-16) for the detection of Rhizoctonia cerealis. 
This invention provides the possibility of assessing potential damage in a specific crop variety-pathogen strain relationship and of utilizing judiciously the diverse armory of fungicides that is available. Furthermore, the invention can be used to provide detailed information on the development and spread of specific pathogen races over extended geographical areas. The invention provides a method of detection that is especially suitable for diseases with a long latent phase.
Kits useful in the practice of the invention are also provided. The kits find particular use in the identification of the fungal pathogen Rhizoctonia cerealis. 
SEQ ID NO:1 Oligonucleotide Primer ITS 1.
SEQ ID NO:2 Oligonucleotide Primer ITS2.
SEQ ID NO:3 Oligonucleotide Primer ITS3.
SEQ ID NO:4 Oligonucleotide Primer ITS4.
SEQ ID NO:5 M13 Universal-20 Primer.
SEQ ID NO:6 Reverse Primer used in Example 2.
SEQ ID NO:7 Oligonucleotide Primer JB643.
SEQ ID NO:8 Oligonucleotide Primer JB644.
SEQ ID NO:9 Oligonucleotide Primer JB645.
SEQ ID NO:10 Oligonucleotide Primer JB646.
SEQ ID NO:11 Oligonucleotide Primer JB647.
SEQ ID NO:12 Oligonucleotide Primer JB648.
SEQ ID NO:13 Oligonucleotide Primer JB649.
SEQ ID NO:14 Oligonucleotide Primer JB650.
SEQ ID NO:15 Oligonucleotide Primer JB687.
SEQ ID NO:16 Oligonucleotide Primer JB688.
SEQ ID NO:17 DNA sequence of the ITS region PCR-amplified from R. cerealis isolate 44235, comprising in the 5xe2x80x2 to 3xe2x80x2 direction: 3xe2x80x2 end of the small subunit rRNA gene (nucleotides 1-30), Internal Transcribed Spacer 1 (nucleotides 31-242), 5.8S rRNA gene (nucleotides 244-395), Internal Transcribed Spacer 2 (nucleotides 397-630), and 5xe2x80x2 end of the large subunit rRNA gene (nucleotides 631-687).
SEQ ID NO:18 DNA sequence of the ITS region PCR-amplified from R. cerealis isolate AGDC57, comprising in the 5xe2x80x2 to 3xe2x80x2 direction: 3xe2x80x2 end of the small subunit rRNA gene (nucleotides 1-30), Internal Transcribed Spacer 1 (nucleotides 31-242), 5.8S rRNA gene (nucleotides 243-395), Internal Transcribed Spacer 2 (nucleotides 396-629), and 5xe2x80x2 end of the large subunit rRNA gene (nucleotides 630-686).
SEQ ID NO:19 DNA sequence of the ITS region PCR-amplified from R. cerealis isolate CAG1BN1, comprising in the 5xe2x80x2 to 3xe2x80x2 direction: 3xe2x80x2 end of the small subunit rRNA gene (nucleotides 1-30), Internal Transcribed Spacer 1 (nucleotides 31-243), 5.8S rRNA gene (nucleotides 244-396), Internal Transcribed Spacer 2 (nucleotides 397-630), and 5xe2x80x2 end of the large subunit rRNA gene (nucleotides 631-687).
SEQ ID NO:20 DNA sequence of the ITS region PCR-amplified from R. cerealis isolate AGDC73, comprising in the 5xe2x80x2 to 3xe2x80x2 direction: 3xe2x80x2 end of the small subunit rRNA gene (nucleotides 1-30), Internal Transcribed Spacer 1 (nucleotides 31-241), 5.8S rRNA gene (nucleotides 242-394), Internal Transcribed Spacer 2 (nucleotides 395-628), and 5xe2x80x2 end of the large subunit rRNA gene (nucleotides 629-685).
SEQ ID NO:21 DNA sequence of the ITS region PCR-amplified from R. cerealis isolate 52182, comprising in the 5xe2x80x2 to 3xe2x80x2 direction: 3xe2x80x2 end of the small subunit rRNA gene (nucleotides 1-30), Internal Transcribed Spacer 1 (nucleotides 31-243), 5.8S rRNA gene (nucleotides 244-396), Internal Transcribed Spacer 2 (nucleotides 397-630), and 5xe2x80x2 end of the large subunit rRNA gene (nucleotides 631-687).
SEQ ID NO:22 DNA sequence of the ITS region PCR-amplified from R. cerealis isolate Bn505, comprising in the 5xe2x80x2 to 3xe2x80x2 direction: 3xe2x80x2 end of the small subunit rRNA gene (nucleotides 1-30), Internal Transcribed Spacer I (nucleotides 31-243), 5.8S rRNA gene (nucleotides 244-396), Internal Transcribed Spacer 2 (nucleotides 397-630), and 5xe2x80x2 end of the large subunit rRNA gene (nucleotides 631-686).
SEQ ID NO:23 DNA sequence of the ITS region PCR-amplified from R. cerealis isolate R88-303, comprising in the 5xe2x80x2 to 3xe2x80x2 direction: 3xe2x80x2 end of the small subunit rRNA gene (nucleotides 1-30), Internal Transcribed Spacer 1 (nucleotides 31-243), 5.8S rRNA gene (nucleotides 244-396), Internal Transcribed Spacer 2 (nucleotides 397-630), and 5xe2x80x2 end of the large subunit rRNA gene (nucleotides 631-687).
SEQ ID NO:24 DNA sequence of the ITS region PCR-amplified from R. cerealis isolate 52184, comprising in the 5xe2x80x2 to 3xe2x80x2 direction: 3xe2x80x2 end of the small subunit rRNA gene (nucleotides 1-30), Internal Transcribed Spacer 1 (nucleotides 31-240), 5.8S rRNA gene (nucleotides 241-393), Internal Transcribed Spacer 2 (nucleotides 394-627), and 5xe2x80x2 end of the large subunit rRNA gene (nucleotides 628-684).
SEQ ID NO:25 DNA sequence of the ITS region PCR-amplified from R. cerealis isolate 62063, comprising in the 5xe2x80x2 to 3xe2x80x2 direction: 3xe2x80x2 end of the small subunit rRNA gene (nucleotides 1-30), Internal Transcribed Spacer I (nucleotides 31-242), 5.8S rRNA gene (nucleotides 243-395), Internal Transcribed Spacer 2 (nucleotides 396-629), and 5xe2x80x2 end of the large subunit rRNA gene (nucleotides 630-686).
SEQ ID NO:26 DNA sequence of the ITS region PCR-amplified from R. cerealis isolate 52183, comprising in the 5xe2x80x2 to 3xe2x80x2 direction: 3xe2x80x2 end of the small subunit rRNA gene (nucleotides 1-30), Internal Transcribed Spacer I (nucleotides 31-242), 5.8S rRNA gene (nucleotides 243-395), Internal Transcribed Spacer 2 (nucleotides 396-629), and 5xe2x80x2 end of the large subunit rRNA gene (nucleotides 630-686).
SEQ ID NO:27 GenBank sequence (accession #AF063019) listing of DNA sequence of the ITS region from R. cerealis, comprising in the 5xe2x80x2 to 3xe2x80x2 direction: 3xe2x80x2 end of the small subunit rRNA gene (nucleotides 1-29), Internal Transcribed Spacer 1 (nucleotides 30-241), 5.8S rRNA gene (nucleotides 242-394), Internal Transcribed Spacer 2 (nucleotides 395-628), and 5xe2x80x2 end of the large subunit rRNA gene (nucleotides 629-685).
SEQ ID NO:28 DNA sequence of the ITS region PCR-amplified from P. herpotrichoides isolate R1, comprising in the 5xe2x80x2 to 3xe2x80x2 direction: 3xe2x80x2 end of the small subunit rRNA gene, Internal Transcribed Spacer 1, 5.8S rRNA gene, Internal Transcribed Spacer 2, and 5xe2x80x2 end of the large subunit rRNA gene.
SEQ ID NO:29 DNA sequence of the ITS region PCR-amplified from S. nodorum isolate 24425, comprising in the 5xe2x80x2 to 3xe2x80x2 direction: 3xe2x80x2 end of the small subunit rRNA gene, Internal Transcribed Spacer 1, 5.8S rRNA gene, Internal Transcribed Spacer 2, and 5xe2x80x2 end of the large subunit rRNA gene.
SEQ ID NO:30 DNA sequence of the ITS region PCR-amplified from S. tritici isolate 26517, comprising in the 5xe2x80x2 to 3xe2x80x2 direction: 3xe2x80x2 end of the small subunit rRNA gene, Internal Transcribed Spacer 1, 5.8S rRNA gene, Internal Transcribed Spacer 2, and 5xe2x80x2 end of the large subunit rRNA gene.
SEQ ID NO:31 DNA sequence of the ITS region PCR-amplified from P. tritici-repentis isolate 6715, comprising in the 5xe2x80x2 to 3xe2x80x2 direction: 3xe2x80x2 end of the small subunit rRNA gene, Internal Transcribed Spacer 1, 5.8S rRNA gene, Internal Transcribed Spacer 2, and 5xe2x80x2 end of the large subunit rRNA gene.
SEQ ID NO:32 DNA sequence of the ITS region PCR-amplified from F. culmorum isolate 62215, comprising in the 5xe2x80x2 to 3xe2x80x2 direction: 3xe2x80x2 end of the small subunit rRNA gene, Internal Transcribed Spacer 1, 5.8S rRNA gene, Internal Transcribed Spacer 2, and 5xe2x80x2 end of the large subunit rRNA gene.
SEQ ID NO:33 DNA sequence of the ITS region PCR-amplified from M. nivale isolate 520, comprising in the 5xe2x80x2 to 3xe2x80x2 direction: 3xe2x80x2 end of the small subunit rRNA gene, Internal Transcribed Spacer 1, 5.8S rRNA gene, Internal Transcribed Spacer 2, and 5xe2x80x2 end of the large subunit rRNA gene.
The present invention provides unique DNA sequences that are useful in identifying different pathotypes of plant pathogenic fungi. Particularly, the DNA sequences can be used as primers in PCR-based analysis for the identification of fungal pathotypes. The DNA sequences of the invention include the Internal Transcribed Spacer (ITS) sequences of the ribosomal RNA gene regions of particular fungal pathogens as well as primers derived from these regions that are capable of identifying the particular pathogen. These ITS DNA sequences from different pathotypes within a pathogen species or genus, which vary between the different members of the species or genus, can be used to identify those specific members.
Biomedical researchers have used PCR-based techniques for some time and with moderate success to detect pathogens in infected animal tissues. Only recently, however, has this technique been applied to detect plant pathogens. The presence of Gaumannomyces graminis in infected wheat has been detected using PCR of sequences specific to the pathogen mitochondrial genome (Schlesser et al., 1991; Applied and Environ. Microbiol. 57: 553-556), and random amplified polymorphic DNA (i.e. RAPD) markers were able to distinguish numerous races of Gremmeniella abietina, the causal agent of scleroderris canker in conifers. U.S. Pat. No. 5,585,238 (incorporated herein by reference in its entirety) describes primers derived from the ITS sequences of the ribosomal RNA gene region of strains of Septoria, Pseudocercosporella, and Mycosphaerella and their use in the identification of these fungal isolates using PCR-based techniques. In addition, WO 95/29260 (herein incorporated by reference in its entirety) describes primers derived from the ITS sequences of the ribosomal RNA gene region of strains of Fusarium and their use in the identification of these fungal isolates using PCR-based techniques. Furthermore, U.S. Pat. No. 5,800,997 (incorporated herein by reference in its entirety) describes primers derived from the ITS sequences of the ribosomal RNA gene region of strains of Cercospora, Helminthosporium, Kabatiella, and Puccinia and their use in the identification of these fungal isolates using PCR-based techniques.
Ribosomal genes are suitable for use as molecular probe targets because of their high copy number. Despite the high conservation between mature rRNA sequences, the non-transcribed and transcribed spacer sequences are usually poorly conserved and are thus suitable as target sequences for the detection of recent evolutionary divergence. Fungal rRNA genes are organized in units, each of which encodes three mature subunits of 18S (small subunit), 5.8S, and 28S (large subunit). These subunits are separated by two Internal Transcribed Spacers, ITS1 and ITS2, of around 300 bp (White et al., 1990; In: PCR Protocols; Eds.: Innes et al.; pages 315-322). In addition, the transcriptional units are separated by non-transcribed spacer sequences (NTSs). The ITS and NTS sequences are particularly suitable for the detection of specific pathotypes of different fungal pathogens.
The DNA sequences of the invention are from the Internal Transcribed Spacer sequences of the ribosomal RNA gene region of different plant pathogens. The ITS DNA sequences from different pathotypes within a pathogen species or genus vary among the different members of the species or genus. Once having determined the ITS sequences of a pathogen, these sequences can be aligned with other ITS sequences. In this manner, primers can be derived from the ITS sequences. That is, primers can be designed based on regions within the ITS sequences that contain the greatest differences in sequence among the fungal pathotypes. These sequences and primers based on these sequences can be used to identify specific pathogens.
Particular DNA sequences of interest include ITS DNA sequences from Rhizoctonia cerealis. Such ITS DNA sequences are disclosed in SEQ ID NOs: 17-26. Sequences of representative oligonucleotide primers derived from these ITS sequences are disclosed in SEQ ID NOs: 7-16. The sequences find use in the PCR-based identification of the pathogen of interest.
Methods for the use of the primer sequences of the invention in PCR analysis are well known in the art. For example, see U.S. Pat. Nos. 4,683,195 and 4,683,202, as well as Schlesser et al. (1991) Applied and Environ. Microbiol. 57:553-556. See also, Nazar et al. (1991; Physiol. and Molec. Plant Pathol. 39: 1-11), which used PCR amplification to exploit differences in the ITS regions of Verticillium albo-atrum and Verticillium dahliae and therefore distinguish between the two species; and Johanson and Jeger (1993; Mycol. Res. 97: 670-674), who used similar techniques to distinguish the banana pathogens Mycosphaerella fijiensis and Mycospharella musicola. 
The ITS DNA sequences of the invention can be cloned from fungal pathogens by methods known in the art. In general, the methods for the isolation of DNA from fungal isolates are known. See, Raeder and Broda (1985) Letters in Applied Microbiology 2:17-20; Lee et al. (1990) Fungal Genetics Newsletter 35:23-24; and Lee and Taylor (1990) In: PCR Protocols: A Guide to Methods and Applications, Innes et al. (Eds.); pages 282-287.
Alternatively, the ITS sequences of interest can be determined by PCR amplification. In an exemplified embodiment, primers to amplify the entire ITS region are designed according to White et al. (1990; In: PCR Protocols; Eds.: Innes et al. pages 315-322), and the amplified ITS sequence are subcloned into the pCR2.1 cloning vector. The subcloned sequence include the left hand ITS (ITS 1), the right hand ITS (ITS2), as well as the centrally located 5.8S rRNA gene. This is undertaken for several isolates of Rhizoctonia cerealis. 
The determined ITS sequences are compared within each pathogen group to locate divergences that might be useful to test in PCR to distinguish the different species and/or strains. Exemplary determined ITS DNA sequences are shown in SEQ ID NOs: 17-26. A comparative alignment is made of these ITS DNA sequences. From the identification of divergences, numerous primers are synthesized and tested in PCR-amplification. Templates used for PCR-amplification testing are firstly purified pathogen DNA, and subsequently DNA isolated from infected host plant tissue. Thus, it is possible to identify pairs of primers that are diagnostic, i.e. that identify one particular pathogen species or strain but not another species or strain of the same pathogen.
Preferred primer combinations are able to distinguish between the different species or strains in infected host tissue, i.e. host tissue that has previously been infected with a specific pathogen species or strain. This invention provides numerous primer combinations that fulfill this criterion for detection of Rhizoctonia cerealis. The primers of the invention are designed based on sequence differences among the fungal ITS regions. A minimum of one base pair difference between sequences can permit design of a discriminatory primer. Primers designed to a specific fungal DNA""s ITS region can be used in combination with a primer made to a conserved sequence region within the ribosomal DNA""s coding region to amplify species-specific PCR fragments. In general, primers should have a theoretical melting temperature between about 60 to about 70 degree xc2x0 C. to achieve good sensitivity and should be void of significant secondary structure and 3xe2x80x2 overlaps between primer combinations. Primers generally have 100% sequence identity with at least about 5-10 contiguous nucleotide bases of ITS 1 or ITS2. In preferred embodiments, primers are anywhere from approximately 5-30 nucleotide bases long.
The present invention lends itself readily to the preparation of xe2x80x9ckitsxe2x80x9d containing the elements necessary to carry out the process. Such a kit may comprise a carrier being compartmentalized to receive in close confinement therein one or more container, such as tubes or vials. One of the containers may contain unlabeled or detectably labeled DNA primers. The labeled DNA primers may be present in lyophilized form or in an appropriate buffer as necessary. One or more containers may contain one or more enzymes or reagents to be utilized in PCR reactions. These enzymes may be present by themselves or in admixtures, in lyophilized form or in appropriate buffers.
Finally, the kit may contain all of the additional elements necessary to carry out the technique of the invention, such as buffers, extraction reagents, enzymes, pipettes, plates, nucleic acids, nucleoside triphosphates, filter paper, gel materials, transfer materials, autoradiography supplies, and the like.
The examples below show typical experimental protocols that can be used in the isolation of ITS sequences, the selection of suitable primer sequences, the testing of primers for selective and diagnostic efficacy, and the use of such primers for disease and fungal isolate detection. Such examples are provided by way of illustration and not by way of limitation.